Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM...1594 days ago
Tadpole: an assembler, error-corrector, and read-extender
Tadpole is a kmer-based assembler, with additional capabilities of error-correcting and extending reads. It does not do any complicated graph...1586 days ago
PANEV: an R package for a pathway-based network visualization
PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on info...m 1 to n) of interconnected upstream and downstream pathways. The network graph...1582 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph...1552 days ago
1519 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS incl...ing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph...1484 days ago
medaka: Sequence correction provided by ONT Research
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using n...pileup of individual sequencing reads against a draft assembly. It outperforms graph-...1483 days ago
1453 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and acyclic while pres...visualization, and reuse of pangenome variation graphs...1364 days ago
Applied Computational Genomics Course at UU: Spring 2020
This course will provide a comprehensive introduction to fundamental concepts and ex...esearch. The primary goal of the course is for students to be grounded in theory and leave the course empowere...1264 days ago